Particles able to settle distances of approximately a meter in 1–2 h are undersampled in water traditionally collected in Niskin bottles. Gardner (Limnol Oceanogr, 22, 764–768, 1977) demonstrated that particles sink into the space below the spout of Niskin bottles on timescales relevant to sample processing. We examined this effect on measurements of microbial abundance, community composition, and transparent stainable particles across an oxygen-sulfide gradient in the Cariaco Basin. Within 1 h, modestly sized micro-aggregates (> 16 lm) were not detected in samples drawn from the spout, but were abundant in the waters below the spout. Total transparent exopolymer particles (TEP) and Coomassie stainable particles (CSP) were at least twice as abundant in the below-spout samples as in spout-collected water. Below-spout samples accounted for four times more total particle surface area per mL than spout samples. Approximately 10% of all microbes were particle-associated, which led to only small enrichments of total microbes in the below-spout samples. However, fluorescent in situ hybridization (FISH) revealed five of seven clades surveyed were significantly more enriched in water below the spout than total cells, indicating (1) a small bias when enumerating total particles and microbes from spout samples and (2) a very strong bias for particular phylogenetic groups that are more prevalent on particles than the total community. In particular, sulfate-reducing δ-proteobacteria were consistently enriched in below-spout samples collected at depths along the oxygen-sulfide transition. Abundance of this functional group has potentially been underestimated in the past. Consequently, microbial diversity results derived from Niskin bottle samples should be cautiously applied when interpreting biogeochemical cycling.